URLhttps://www.bco-dmo.org/dataset/781114
Download URLhttps://www.bco-dmo.org/dataset/781114/data/download
Media Typetext/tab-separated-values
CreatedNovember 6, 2019
ModifiedNovember 22, 2019
StateFinal no updates expected
Brief Description16S rRNA gene (from RNA)

Acquisition Description

Sampling of cores was done in accordance with IODP protocols.

All C0014 samples were cored on 16 September 2010 via via HPCS (hydraulic piston coring system).
All C0015 samples were cored on 18 September 2010 via HPCS.
All C0017 samples were cored on 27 September 2010 via HPCS.

Core sections were kept frozen (-80°C) until DNA extractions. RNA was extracted using a phenol chloroform protocol. The RNA extract was DNAse treated using the Invitrogen™ Ambion™ Turbo DNA-free Kit and purified using the Qiagen® RNeasy Mini Kit. A cDNA library was made using the Qiagen ® QuantiTec Reverse Transcription Kit. Polymerase chain reactions used the KAPABiosystems® KAPA2G Robust HotStart ReadyMix PCR Kit for 32 cycles.

Sequencing of the product was performed on the Illumina® MiSeq 2500.

Processing Description

Data Processing: Demultiplexing was performed in Mothur (v.1.30.1).

Problem report: Upon analysis, the RNA dataset does not appear to reflect the same or similar information as the published 16S rRNA gene amplicon dataset. Rather, it indicates significant background noise from extraction and not an indigenous representation of the subsurface biosphere.

Instruments

Illumina MiSeq 2500 [Automated DNA Sequencer]
Details

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

hydraulic piston coring system (HPCS) [Advanced Piston Corer]
Details

The JOIDES Resolution's Advanced Piston Corer (APC) is used in soft ooze and sediments. The APC is a hydraulically actuated piston corer designed to recover relatively undisturbed samples from very soft to firm sediments.

More information is available from IODP (PDF).

Parameters

Cruise_ID [cruise_id]
Details
Cruise_ID
Cruise ID number
cruise designation; name
Sample_Name [sample]
Details
Sample_Name
Sample name

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

Water_depth [depth_w]
Details
Water_depth
Water depth

water depth, in meters

Top_Depth [depth_bsf]
Details
Top_Depth
Top depth

depth below seafloor.  Includes mbsf (meters below seafloor) and cmbsf (centimeters below seafloor).

Bottom_Depth [depth_bsf]
Details
Bottom_Depth
Bottom depth

depth below seafloor.  Includes mbsf (meters below seafloor) and cmbsf (centimeters below seafloor).

Sediment_type [sample_descrip]
Details
Sediment_type
Sediment type
text description of sample collected
Estimated_Temp [temperature]
Details
Estimated_Temp
Estimated temperature; based on 3 degrees C/m
water temperature at measurement depth
Nucleic_Acid_amplified [sample_descrip]
Details
Nucleic_Acid_amplified
Type of nucleic acid amplified
text description of sample collected
Primer_Set_16S_rRNA [sample_descrip]
Details
Primer_Set_16S_rRNA

16S rRNA primer set

text description of sample collected
Illumina_dataset [sample_descrip]
Details
Illumina_dataset
Illumina dataset ID
text description of sample collected
Notes [comment]
Details
Notes
Notes
free text comments, may only have meaning to submitting PI

Dataset Maintainers

NameAffiliationContact
Christopher H. HousePennsylvania State University (PSU)
Leah D. BrandtPennsylvania State University (PSU)
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project TitleAn In-Depth analysis of the subvent biosphere within Okinawa Backarc Basin (IODP 331, Iheya North Hydrothermal Field) sediments
AcronymSubvent_Biosphere_Sediments
URLhttps://www.bco-dmo.org/project/714230
CreatedSeptember 1, 2017
ModifiedNovember 5, 2019
Project Description

The Iheya North Hydrothermal Field in the Okinawa Backarc Basin represents an ideal environment in which to investigate the biotic temperature fringe of microbial life at depth because of its subsurface hydrothermal activity within its continental margin-type sediment profile. Geographically, the Okinawa Backarc Basin is situated along a continental margin, which is a sediment profile type commonly sampled and studied across the seafloor (e.g. Peru Margin, Costa Rica Margin, Cascadia Margin). The hydrothermal network within the subsurface here supplies an additional temperature obstacle to microbial life existing in the sediments. In particular, the sediment profile at Site C0014 exhibits a transition from hemipelagic ooze with pumiceous volcaniclastic sediments and low temperature (4°C) to a hydrothermally altered sequence of clays within the top ~10 mbsf of sediment. Temperature measurements indicate a gradient of approximately 3°C/m, which is roughly an order of magnitude greater than continental margin sites (e.g. Cascadia Margin, IODP 311 and Costa Rica Margin, IODP 344), but is more gradual than intense, centimeter-scale gradients from other hot, surface sediments. We have focused on the application of culture-independent, molecular methods to understand taxonomic and functional characteristics through this hydrothermal gradient. Confidence in DNA recovery suggests a microbial biosphere extent of approximately 15 mbsf (55°C).

Results from both 16S rRNA gene surveys and metagenomics analyses suggest a temperature-dependent stratigraphy of taxonomic and functional adaptations between the shallowest and deepest sample horizons. Cosmopolitan marine subsurface bacterial and archaeal taxa are present throughout the top 10 mbsf, whereas, hyperthermophilic heterotrophic as well as thermophilic anaerobic methanotrophic archaea appear in varying local abundances in deeper, hydrothermal clay horizons. "An In-Depth analysis of the subvent biosphere within Okinawa Backarc Basin (IODP 331, Iheya North Hydrothermal Field) sediments" encompasses datasets funded through C-DEBI to investigate the microbial communities in IODP 331 Iheya North Hydrothermal Field sediments. Site C0014 at this field site is 500 m away from the active vent and experiences a 3C/m temperature gradient with depth. In the research grant "Investigating the active microbial populations in near hydrothermal vent sediments" and the Research Exchange grant "Learning new RNA extraction techniques", we used an RNA-based approach to explore the active microbial community. Upon analysis, the RNA dataset does not appear to reflect the same information as the phylogenetic signals coming from both the 16S rRNA gene as well as the metagenomes. The data indicate significant background noise from the RNA extraction process rather than from an indigenous representation of the subsurface biosphere.

The graduate fellowship "An in-depth analysis of the subvent biosphere within the Okinawa backarc basin Iheya North hydrothermal field" provided an opportunity to bring together metagenomic, 16S rRNA gene amplicon (DNA), and 16S rRNA amplicon datasets from IODP 331 Iheya North Hydrothermal Field sediments to understand the biogeography of this subvent biosphere.

For more information, refer to the following C-DEBI grants/projects.
An in-depth analysis of the subvent biosphere within the Okinawa backarc basin Iheya North hydrothermal field:
https://www.darkenergybiosphere.org/award/an-in-depth-analysis-of-the-subvent-biosphere-within-the-okinawa-backarc-basin-iheya-north-hydrothermal-field/

Investigating the active microbial populations in near hydrothermal vent sediments: https://www.darkenergybiosphere.org/award/investigating-the-active-microbial-populations-in-near-hydrothermal-vent-sediments/

Learn new RNA extraction techniques: https://www.darkenergybiosphere.org/award/learn-new-rna-extraction-techniques/
 

Project Maintainers
NameAffiliationRoleContact
Christopher H. HousePennsylvania State University (PSU)Principal Investigator
Jennifer F. BiddleUniversity of DelawareCo-Principal Investigator
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